A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of R...A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of RNA2 sequence of MrNV.The 224 bp specific amplification product was obtained in positive sample determined with 3%agarose gel electrophoresis,while no product was generated from shrimp infected with other viruses including DNA viruses（IHHNV,WSSV）and RNA viruses（TSV,IMNV,YHV）.The detecting limit of the assay was 8pg nucleic acid,which is more sensitive than that of PCR method.展开更多
Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing me...Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods-sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GP=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.展开更多
This paper develops sequence-based methods for identifying novel protein-protein interactions （PPIs） by means of support vector machines （SVMs）. The authors encode proteins ont only in the gene level but also in t...This paper develops sequence-based methods for identifying novel protein-protein interactions （PPIs） by means of support vector machines （SVMs）. The authors encode proteins ont only in the gene level but also in the amino acid level, and design a procedure to select negative training set for dealing with the training dataset imbalance problem, i.e., the number of interacting protein pairs is scarce relative to large scale non-interacting protein pairs. The proposed methods are validated on PPIs data of Plasmodium falciparum and Escherichia coli, and yields the predictive accuracy of 93.8% and 95.3%, respectively. The functional annotation analysis and database search indicate that our novel predictions are worthy of future experimental validation. The new methods will be useful supplementary tools for the future proteomics studies.展开更多
Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms,which may serve as promising sources of enzymes and natural products for industrial applications.Identifying enzymes...Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms,which may serve as promising sources of enzymes and natural products for industrial applications.Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools.The catalytic properties of all enzymes are primarily dictated by their structures,which are predominantly determined by their amino acid sequences.However,this aspect has not been fully considered in the enzyme bioprospecting processes.With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts,structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties.Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise.Here,we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates,in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.展开更多
Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed...Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed Tit (Parus monticolus) to explore the resolving ability of these two types of markers. The south-western and central mitochondrial DNA (mtDNA) phylogroups were divergent to some extent in sequence-based nuclear data, while mixed together in microsatellites data. The F ST values among clades were about four times lower in microsatellite loci than those in sequence-based nuclear loci. We are of the opinion that size homoplasy may have contributed to the inability of microsatellites to uncover differentiation. Our results suggest that sequence-based nuclear loci outperformed microsatellite loci in detecting population structures, especially those focused on populations with large effective population sizes. There was no significant correlation between F ST values and allelic size variability, which suggested that the efficiency of microsatellite loci in detecting genetic structure may be independent of their polymorphism. F ST is better than R ST in detecting intraspecific divergence due to the high variance of R ST . In agreement with sequence-based nuclear loci, microsatellite loci did resolve the genetic distinctness of the Taiwan Residents phylogroup. The genetic differentiation between the Taiwan Residents and continental clades may involve allopatric divergence without gene flow.展开更多
Nucleic acid(DNA and RNA)detection and quantification methods play vital roles in molecular biology.With the development of molecular biology,isothermal amplification of DNA/RNA,as a new molecular biology technology,c...Nucleic acid(DNA and RNA)detection and quantification methods play vital roles in molecular biology.With the development of molecular biology,isothermal amplification of DNA/RNA,as a new molecular biology technology,can be amplified under isothermal condition,it has the advantages of high sensitivity,high specificity,and high efficiency,and has been applied in various fields of biotechnology,including disease diagnosis,pathogen detection,food hygiene and safety detection and so on.This paper introduces the progress of isothermal amplification technology,including rolling circle amplification(RCA),nucleic acid sequence-dependent amplification(NASBA),strand displacement amplification(SDA),loop-mediated isothermal amplification(LAMP),helicase-dependent amplification(HDA),recombinase polymerase amplification(RPA),cross-priming amplification(CPA),and its principle,advantages and disadvantages,and application development are briefly summarized.展开更多
Objective:To determine patterns of antimicrobial resistance,analyze the prevalence of oxacillinase and molecular typing of strains of Acinetobacter baumannii(A.baumannii).Methods:A total of 121 strains of A.baumannii ...Objective:To determine patterns of antimicrobial resistance,analyze the prevalence of oxacillinase and molecular typing of strains of Acinetobacter baumannii(A.baumannii).Methods:A total of 121 strains of A.baumannii were obtained from patients admitted to Imam Hossein and Imam Khomeini Hospitals,Tehran,Iran,from January 2016 to November 2018.Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method according to the Clinical and Laboratory Standards Institute recommendations.The presence of oxacillinase genes was assessed by polymerase chain reaction(PCR).To determine clonal relatedness,all isolates were subjected to repetitive sequence-based PCR(REP-PCR).Results:The isolates were obtained from 56(46.3%)males and 65(53.7%)females with the mean age of 39.5 years.Colistin with 100.0%sensitivity rate had the highest effect,while ceftriaxone with 16.5%sensitivity rate had the least effect on A.baumannii isolates.In addition,96(79.3%)and 99(81.8%)isolates were resistant to imipenem and meropenem,respectively.A total of 109 isolates(90.0%)exhibited multiple drug resistance with 10 different resistotypes.In total,75(75.7%)of carbapenem resistant isolates were positive for blaOXA-23-like,and 14(14.1%)for blaOXA-24-like gene.The five main clones A,B,C,D,and E were detected in 25(25.2%),36(36.4%),10(10.1%),8(8.0%),and 6(6.1%)of isolates,respectively.Conclusions:Carbapenem-resistant A.baumannii strains are high in the current study.To control the spread of carbapenem-resistant A.baumannii strains,regular monitoring programs are needed.展开更多
Tsukamurella species are obligate aerobic,gram-positive,weak acid-fast,nonmotile bacilli.They are found in various environments,such as soil,water,sludge,and petroleum reservoir wastewater,and belong to the order Acti...Tsukamurella species are obligate aerobic,gram-positive,weak acid-fast,nonmotile bacilli.They are found in various environments,such as soil,water,sludge,and petroleum reservoir wastewater,and belong to the order Actinomycetales.In 2016,there was a reclassification of species within the genus Tsukamurella,merging the species Tsukamurella tyrosinosolvens(T.tyrosinosolvens)and Tsukamurella carboxydivorans.Tsukamurella species are clinically considered to be a rare opportunistic pathogen,because most reported cases have been related to bacteremia and intravascular prosthetic devices and immunosuppression.To date,it has been isolated only from human specimens,and has always been associated with clinical disease;human infections are very rare.Reported infections have included pneumonia,brain abscesses,catheter-related bloodstream infections,ocular infections,bacteremia,and sepsis presenting with septic pulmonary emboli in patients who are immunocompromised.To date,there is no commercially available test for identification.On the other hand,sequence-based identification,including matrix-assisted laser desorption ionization time-of-flight mass spectrometry,is an alternative method for identifying clinical isolates that are either slow growers or difficult to identify through biochemical profiling.The golden standards for diagnosis and optimal management still remain to be determined.However,newer molecular biological techniques can provide accurate identification,and contribute to the appropriate selection of definitive therapy for infections caused by this organism.Combinations of several antimicrobial agents have been proposed for treatment,though the length of treatment for infections has yet to be determined,and should be individualized according to clinical response.Immunocompromised patients often experience severe cases due to infection,and life-threatening T.tyrosinosolvens events associated with dissemination and/or failure of source control have occurred.Favorable prognoses can be achieved through earlier identification of the cause of infection,as well as successful management,including appropriate antibiotic therapy together with source control.Further analyses of similar cases are required to establish the most adequate diagnostic methods and treatment regimens for infections.展开更多
基金Supported by Special Fund for Agro-scientific Research in the Public Interest(201103034)Huzhou Science and Technology Project(2012GN08,2011ZD2005)Science and Technology Innovation Team Project of Freshwater Aquaculture of Zhejiang Province(2012R10026-11)
文摘A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of RNA2 sequence of MrNV.The 224 bp specific amplification product was obtained in positive sample determined with 3%agarose gel electrophoresis,while no product was generated from shrimp infected with other viruses including DNA viruses（IHHNV,WSSV）and RNA viruses（TSV,IMNV,YHV）.The detecting limit of the assay was 8pg nucleic acid,which is more sensitive than that of PCR method.
文摘Human leukocyte antigen (HLA) system is the most polymorphic region known in the human genome. In the present study, we analyzed for the first time the HLA-A gene polymorphisms defined by the high-resolution typing methods-sequence-based typing (SBT) in 161 Northern Chinese Han people. A total of 74 different HLA-A gene types and 36 alleles were detected. The most frequent alleles were A*110101 (GP=0.2360), A*24020101 (GF=0.1646), and A*020101 (GF=0.1553); followed by A*3303 (GF=0.1180), A*3001 (GF=0.0590), and A*310102 (GF=0.0404). The frequencies of following alleles, A*0203, A*0205, A*0206, A*0207, A*030101, A*2423, A*2601, A*3201, and A*3301, are all higher than 0.0093. The homozygous alleles include A*020101, A*110101, A*24020101 and A*310102. Heterozygosity (H), polymorphism information content (PIC), discrimination power (DP) and probability of paternity exclusion (PPE) of HLA-A in the samples were calculated and their values were 0.8705, 0.8491, 0.6014, and 0.9475, respectively. These results by SBT analysis of HLA-A polymorphism in Northern Chinese Han population, especially the allele subtypes character, will be of great interest for clinical transplantation, disease-associated study and forensic identification. Implementation of high-resolution typing methods allows a significantly wider spectrum of HLA variation including rare alleles. This spectrum will further be extensively utilized in many fields.
基金This research is supported by the Key Project of the National Natural Science Foundation of China under Grant No. 10631070, the National Natural Science Foundation of China under Grant Nos. 10801112, 10971223, 11071252, and the Ph.D Graduate Start Research Foundation of Xinjiang University Funded Project under Grant No. BS080101. Thank Dr. Yong Wang from Institute of Systems Science, Academy of Mathematics and Systems Science for kind discussion and good suggestions.
文摘This paper develops sequence-based methods for identifying novel protein-protein interactions （PPIs） by means of support vector machines （SVMs）. The authors encode proteins ont only in the gene level but also in the amino acid level, and design a procedure to select negative training set for dealing with the training dataset imbalance problem, i.e., the number of interacting protein pairs is scarce relative to large scale non-interacting protein pairs. The proposed methods are validated on PPIs data of Plasmodium falciparum and Escherichia coli, and yields the predictive accuracy of 93.8% and 95.3%, respectively. The functional annotation analysis and database search indicate that our novel predictions are worthy of future experimental validation. The new methods will be useful supplementary tools for the future proteomics studies.
基金Funding was provided by the Agricultural Biotechnology Research Institute of Iran(ABRII),Swedish Research Council(Vetenskapsrådet grant no.:2017-05019)the BBSRC Institute Strategic Programme Gut Microbes and Health(BB/r012490/1,its constituent project BBS/e/F/000Pr10355).
文摘Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms,which may serve as promising sources of enzymes and natural products for industrial applications.Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools.The catalytic properties of all enzymes are primarily dictated by their structures,which are predominantly determined by their amino acid sequences.However,this aspect has not been fully considered in the enzyme bioprospecting processes.With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts,structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties.Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise.Here,we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates,in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.
基金supported by the National Science Fund for Distinguished Young Scientists (No. 30925008)the Major International (Regional) Joint Research Project (No. 31010103901)+1 种基金the CAS-IOZ Innovation Program (KSCX2-EW-J-2) by a grant (No. O529YX5105) from the Key Laboratory of the Zoological Systematics and Evolution of the Chinese Academy of Sciences to F.M. Lei
文摘Although a growing number of both sequence-based and microsatellite nuclear loci have been used to infer genetic structures, their relative efficiencies remain poorly understood. In our study, we used the Green-backed Tit (Parus monticolus) to explore the resolving ability of these two types of markers. The south-western and central mitochondrial DNA (mtDNA) phylogroups were divergent to some extent in sequence-based nuclear data, while mixed together in microsatellites data. The F ST values among clades were about four times lower in microsatellite loci than those in sequence-based nuclear loci. We are of the opinion that size homoplasy may have contributed to the inability of microsatellites to uncover differentiation. Our results suggest that sequence-based nuclear loci outperformed microsatellite loci in detecting population structures, especially those focused on populations with large effective population sizes. There was no significant correlation between F ST values and allelic size variability, which suggested that the efficiency of microsatellite loci in detecting genetic structure may be independent of their polymorphism. F ST is better than R ST in detecting intraspecific divergence due to the high variance of R ST . In agreement with sequence-based nuclear loci, microsatellite loci did resolve the genetic distinctness of the Taiwan Residents phylogroup. The genetic differentiation between the Taiwan Residents and continental clades may involve allopatric divergence without gene flow.
基金supported by grants from Jiangsu Higher Education Institution Innovative Research Team for Science and Technology(2021),the Key Technology Program of Suzhou People’s Livelihood Technology Projects(Grant Nos.SKY2021029,SZS2020311)the Open Project of Jiangsu Biobank of Clinical Resources(TC2021B009)the Qing-Lan Project of Jiangsu Province in China(2021,2022).
文摘Nucleic acid(DNA and RNA)detection and quantification methods play vital roles in molecular biology.With the development of molecular biology,isothermal amplification of DNA/RNA,as a new molecular biology technology,can be amplified under isothermal condition,it has the advantages of high sensitivity,high specificity,and high efficiency,and has been applied in various fields of biotechnology,including disease diagnosis,pathogen detection,food hygiene and safety detection and so on.This paper introduces the progress of isothermal amplification technology,including rolling circle amplification(RCA),nucleic acid sequence-dependent amplification(NASBA),strand displacement amplification(SDA),loop-mediated isothermal amplification(LAMP),helicase-dependent amplification(HDA),recombinase polymerase amplification(RPA),cross-priming amplification(CPA),and its principle,advantages and disadvantages,and application development are briefly summarized.
文摘Objective:To determine patterns of antimicrobial resistance,analyze the prevalence of oxacillinase and molecular typing of strains of Acinetobacter baumannii(A.baumannii).Methods:A total of 121 strains of A.baumannii were obtained from patients admitted to Imam Hossein and Imam Khomeini Hospitals,Tehran,Iran,from January 2016 to November 2018.Antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion method according to the Clinical and Laboratory Standards Institute recommendations.The presence of oxacillinase genes was assessed by polymerase chain reaction(PCR).To determine clonal relatedness,all isolates were subjected to repetitive sequence-based PCR(REP-PCR).Results:The isolates were obtained from 56(46.3%)males and 65(53.7%)females with the mean age of 39.5 years.Colistin with 100.0%sensitivity rate had the highest effect,while ceftriaxone with 16.5%sensitivity rate had the least effect on A.baumannii isolates.In addition,96(79.3%)and 99(81.8%)isolates were resistant to imipenem and meropenem,respectively.A total of 109 isolates(90.0%)exhibited multiple drug resistance with 10 different resistotypes.In total,75(75.7%)of carbapenem resistant isolates were positive for blaOXA-23-like,and 14(14.1%)for blaOXA-24-like gene.The five main clones A,B,C,D,and E were detected in 25(25.2%),36(36.4%),10(10.1%),8(8.0%),and 6(6.1%)of isolates,respectively.Conclusions:Carbapenem-resistant A.baumannii strains are high in the current study.To control the spread of carbapenem-resistant A.baumannii strains,regular monitoring programs are needed.
文摘Tsukamurella species are obligate aerobic,gram-positive,weak acid-fast,nonmotile bacilli.They are found in various environments,such as soil,water,sludge,and petroleum reservoir wastewater,and belong to the order Actinomycetales.In 2016,there was a reclassification of species within the genus Tsukamurella,merging the species Tsukamurella tyrosinosolvens(T.tyrosinosolvens)and Tsukamurella carboxydivorans.Tsukamurella species are clinically considered to be a rare opportunistic pathogen,because most reported cases have been related to bacteremia and intravascular prosthetic devices and immunosuppression.To date,it has been isolated only from human specimens,and has always been associated with clinical disease;human infections are very rare.Reported infections have included pneumonia,brain abscesses,catheter-related bloodstream infections,ocular infections,bacteremia,and sepsis presenting with septic pulmonary emboli in patients who are immunocompromised.To date,there is no commercially available test for identification.On the other hand,sequence-based identification,including matrix-assisted laser desorption ionization time-of-flight mass spectrometry,is an alternative method for identifying clinical isolates that are either slow growers or difficult to identify through biochemical profiling.The golden standards for diagnosis and optimal management still remain to be determined.However,newer molecular biological techniques can provide accurate identification,and contribute to the appropriate selection of definitive therapy for infections caused by this organism.Combinations of several antimicrobial agents have been proposed for treatment,though the length of treatment for infections has yet to be determined,and should be individualized according to clinical response.Immunocompromised patients often experience severe cases due to infection,and life-threatening T.tyrosinosolvens events associated with dissemination and/or failure of source control have occurred.Favorable prognoses can be achieved through earlier identification of the cause of infection,as well as successful management,including appropriate antibiotic therapy together with source control.Further analyses of similar cases are required to establish the most adequate diagnostic methods and treatment regimens for infections.
